Probably your vent lines.
You need to run two of the vent lines up under the seat.
Besides there is usually always a way around the deep stuff.
Come on up.

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I have 'em routed through one of those fancy-smancy carb vent filter thingees and have the intake lines up under the seat. I think I just got in too deep last time and sucked a bit of water in through the carb... I'm really glad the motor died before it hydro-locked.